The Scleroderma Chronicles: Chasing down the Cytokines

There was more response than I expected from my last post about my efforts to obtain a better understanding about my chronic conditions, the new drugs I was taking, and how to lower my inflammation. I offered in that post to share the links that I used to figure out what foods impact the levels of cytokines that are important in my systemic sclerosis. I’ve gotten feedback/requests for the spreadsheet with my links that I used in my adventures at PubMed.

I’ve been thinking about this for a couple of days, and I think that the most useful thing to do would be to share my process as I hunted down information about cytokines involved in my systemic sclerosis (SSc), and the cytokines that I needed to pay attention to in my diet.

I started out asking: What are the cytokines involved in systemic sclerosis? I did searches using terms like cytokines and systemic sclerosis. Here are some of the links to papers that I found.

I kept a list of the cytokines that were being measured in these studies and I finally began to get a sense of the four big players that were being measured and considered as targets for therapy: Tumor Necrosis Factor alpha (TNFα), Interferon gamma (IFN-γ), Interleukin-6 (IL-6), and Interleukin-1beta (IL-1β). You can follow the same process to research any inflammatory disease that you are interested in; you may get different results. (For example, C-Reactive Protein, called CRP for short, features in many inflammatory conditions. For little SSc me, not so much… my levels are normal.) Anyway, once I had the cytokines of interest, I did searches on all 4 of them. Here’s my info on TNF-α.

InformationSource
TNF-α is also a potent inflammatory mediator and apoptosis inducerThe role of Tumor Necrosis Factor-alpha (TNF-α) in the pathogenesis of systemic lupus erythematosus
Produced by activated immune cells (macrophages, NK cells, T-cells) known to trigger a series of various inflammatory molecules, including other cytokines and chemokines The Role of Tumor Necrosis Factor Alpha (TNF-α) in Autoimmune Disease and Current TNF-α Inhibitors in Therapeutics
TNF-α causes other immune response cells to produce IL-1 and IL-6Tumor necrosis factor – Wikipedia
My question: What does TNF-α do?

I did the same for the other three cytokines and it turns out that for me, it is best to reduce all of them in my blood. At this point I made a little chart with the 4 cytokines at the top and began to do searches on different foods that I thought were anti-inflammatory.

FoodTNFαIFN-γIL-6IL-1β
Chile (Capsaicin)
Tart Cherry
Tomatoes (Lycopene)
Question: Which foods/supplements will decrease these cytokines levels

Now the searching gets easy. I just typed in the questions in the search bar like, “Does capsaicin reduce TNFα” or maybe “Does capsaicin reduce cytokines” and the answer would quickly pop up with some resources. Warning: the search engine will give you the pertinent text and then you are on your own as you search through these papers! If you just go with the fast answers, you will take some risks… I told my sister that tomatoes were bad because I didn’t read the whole text, and I’m not sure if she has forgiven me yet…

Anyway, here are some papers about the foods/supplements above:

If I found a source that said one of the cytokines was reduced by one of my targeted foods, I just put an “X” in that box and moved on. I was no longer recording all of the links in my excitement, and as I found info it sometimes confirmed previous finds, but not always. If I got contradictory information, I was forced to read whole papers. Ugh. Also, you might want to try a different search engine; I used Chrome on my phone and Explorer on the computer, which is another reason for incomplete links on the computer. For the three foods in the table above it ended looking like this.

FoodTNFαIFN-γIL-6IL-1β
Chile (Capsaicin)xx
Tart Cherryxx
Tomatoes (Lycopene)xxx
Question: Which foods/supplements will decrease these cytokines levels

I hope this unpacks the process that I used and helps with any searches that you decide to do that are specific to your own needs/interests.

Happy Caturday!!

The Scleroderma Chronicles: Song of the Cell, Dance of the Cytokines

I’m reading a really wonderful book right now that is really speaking to me on so many levels.

This man is a BioGeek of the first order! He interweaves his experiences, patients, memories, and the history of cells together in a way that makes me green with envy. He unpacks the history of our understanding of cells by bringing those scientists to life in a way that makes me care about them; if only I could write that well. He is the teacher that I wish I had been as he reveals to us how cells work together to create complex human systems, and then ties all of that to the treatment of disease. I’m still in the first parts of the book, but I have already filled my kindle with highlights and notes.

This book was published at the exact right moment when I needed it. I have totally gone down the rabbit hole at PubMed over the last two weeks as I have read paper after paper while chasing down the major players in my chronic conditions (why am I sick, and what exactly are these new meds doing…) and how they link to inflammation. Why would anyone do something like this?

Well, it all comes down to this. I’m on high-risk drugs with some serious side effectss, and I want to make informed decisions about whether I continue taking them. I also had a run-in with elderberry juice, and was rescued by green chile; as a BioGeek I was sucked down the curiosity rabbit hole after that whole adventure. What? That doesn’t happen to you? Listen, it has been so bad I haven’t even been knitting!!!

These are the two drugs that I’m trying to understand. In his book Siddhartha Mukherjee argues that our understanding of cells, and how they work, has transformed medicine into the modern miracle that I am currently benefiting from. Drugs that directly interact with the molecular machinery of cells, the signals between them and the biochemical pathways that cells use to function, are the first of the major transformative directions modern medicine is taking in the treatment of so many pathologies such as cancer, diabetes, neurological, and autoimmune diseases such as mine.

Systemic sclerosis is really darn complicated, as it turns out, and the sequence of events that have been happening in my body are so convoluted it’s hard to track them all. It started in the cells lining my blood vessels. As those cells got injured, they sent out signals that activated parts of my immune system. Signals from the immune cells caused other cells to transform and they began to produce scar tissue… scleroderma means “hard skin”, the hallmark of my condition. Whew. Here’s a condensed version of all that if you want to torture yourself and/or fall asleep.

Let’s go back to my meds. Ambrisentan blocks a molecule that is involved in making blood vessels constrict and raises blood pressure when it is active. That molecule, endothelin, is getting turned off by the drug, and there is evidence that this will improve my exercise-induced pulmonary hypertension and will also keep it from progressing; it plays nice with my other pulmonary hypertension drug which shuts down an enzyme pathway involved in blood pressure. Ofev is my new (fairy dust) drug, and it disables some of the essential enzymes in the cells of my lungs that are involved in creating scar tissue. Interstitial lung disease is currently the leading cause of death for systemic sclerosis patients; mine is being treated by side railing the process in the cells that are essential players in the pathology.

Yay! Molecular trickery at the cellular level saves the day! I will be staying on these meds as long as I can.

Dancing to the tune of the song of immune system cells are cytokines, the messenger molecules that travel between immune system cells and other cells that they interact with. The dance is complex, with all the different messengers traveling through the blood to target cells in the body, latching on and causing the cells to take actions. Some cytokines increase inflammation, and other will shut it down. Your immune system can get dialed up or shut down, depending on what the messages are. In my travels through research papers at PubMed I focused first on what cytokines were involved in systemic sclerosis, and then I hunted for papers that had measured the levels of these cytokines when people ate different foods.

Foods that you consume can make a big difference, evidently. Elderberry made me much worse (I cried in two different doctor’s offices), and green chile saved the day. I was done doing google searches for “anti-inflammatory foods” and was going after hard data.

.What did you expect? I’m a BioGeek. OF COURSE I made a spreadsheet with the data!

Tumor Necrosis Factor alpha (TNFα) is a big driver in the whole systemic sclerosis story along with Interferon gamma (IFN-γ). They cause an increase in two more cytokines that promote inflammation, Interleukin-6 (IL-6) and Interleukin-1 beta (IL-1β). All four of these bad boys will make my inflammation worse and (probably… I’m guessing here) encourage my conditions to progress. A lot of these foods/supplements will lower the levels of these cytokines, which explains why I feel better when I eat them. ELDERBERRY increases three of these cytokines which is why I felt like death warmed over while drinking it. Google said it was anti-inflammatory… can you see why I switched to research papers and cytokines? Green chile stew has tomatoes and green chile in it (and some yummy pork and garlic!); no wonder it turned things around. I will try to eat as many of the “good” foods as I can, but I’m going to focus on ones that really shut down TNFα and IL-6. I’m ignoring the IL-10 and CRP info because it wasn’t really as well supported as the others, and I know that my CRP (C-Reactive Protein) levels are normal.

My lunch smoothie: tart cherries, raspberries, banana, spinach, yogurt, chia seed (gag) and cranberry juice. For dinner I’m having a green chile cheesy corn pudding thing that tastes pretty darn good.

Wow. Did you read all of that stuff above? You deserve a prize for perseverance.

Here’s your prize. It’s like a “Where’s Waldo” picture, but this one is Where’s Hannah!

So, there is all is. Inside my systemic sclerosis, pulmonary hypertension, interstitial lung disease self, there are all these dancing cytokines, following the song of cells. Scientists who were captured by all of this and who were entranced by the Song of the Cell have developed the drugs that are treating the two life-threatening complications of systemic sclerosis that have come my way. Inside me, the promise of the song goes on.

Time to get back to my book.

Notes:

  • Okay, I made a whole other spreadsheet with links to all of the research papers that I used to get some understanding about these cytokines, and which were important in my disease. You don’t want to see all of that, right? If you do, say so in a comment and I’ll send some links your way!
  • I became curious about what is happening with Covid patients and the cytokine storm that can cause severe symptoms. Yep. It’s happening because of TNFα, IFN-γ, and IL-6. If you catch Covid, I don’t recommend elderberry.
  • Clinical trials are currently underway to see if an IL-6 inhibitor will be an effective treatment for systemic sclerosis.
  • I’m a lucky, lucky girl. I have a degree in molecular biology, used to work in an immunology lab that focused on IL-1, was involved in a scleroderma research project, and finished up my lab days on a project looking at the impact of capsaicin on rheumatoid arthritis. I can almost understand what I’m reading on PubMed. Almost.

The BioGeek Memoirs: Ladybug and Aphid

It has suddenly gotten cold here, and I had to bring in plants from outside when we had a hard frost Sunday night. This morning there was a ladybug on the kitchen wall near the ceiling. It was early, I hadn’t had my morning latte yet, and my knees weren’t all that interested in climbing up on the counter to catch the ladybug.

That big jade plant used to be on my front porch.

I’m pretty sure that the ladybug caught a ride into the house on one of the two jade plants that I brought in for the winter. Poor thing. I looked for it later when I was fully caffeinated, and my knees were warmed up, but it was gone. Poor thing. I’ll keep looking for it, but chances are the cats are on the job and its days are numbered.

This is a ladybug. You may know them as ladybird beetles or ladybirds.

They are all over the yard at the moment. I found several while getting the leaves raked up last week and I’m hoping that I didn’t put any of them in the trash bags with the leaves. They are cute, right? I bet you used to catch them and did the “Ladybug, ladybug, fly away home…” thing with them too. I just loved ladybugs as a kid and loved to watch them lift their bright spotted elytra (wing covers) as they took to flight from off my pudgy little kid finger.

You’d never know that they were relentless predators, right?

See all of those aphids on my rose? I needed some ladybugs to come take care of this for me!!!

That’s right, ladybugs prey on aphids. Yay, ladybugs! You may not recognize them on the bushes while they are on the hunt because a lot of the munching happens in the nymph form, and they look kind of like alien spiders of some type. You remember learning about the butterfly life cycle, right? Ladybugs are somewhat the same with the nymphs being the hungry caterpillar equivalent.

I used to use ladybugs and aphids in my teaching because they are good examples of sexual and asexual reproduction. Ladybugs mate between males and females to combine DNA from both parents in the offspring, and aphids do that too, but the reason they can take over the garden so quickly is because they mostly are reproducing without any mating and can produce ridiculous numbers of offspring within weeks as the new females (yep, they are all females) lay even more eggs and you can get a rose like mine above before you even know you have a problem. This is why I wanted to return that kitchen ladybug back to the garden outside.

(Are you wondering if I showed pictures of ladybugs mating to my biology students? Of course, I did! If you had to teach meiosis to 16 year-old teenagers who were becoming bored out of their minds, you would have too!!)

Every once in a while, the ladybugs get out of control and swarm here in Colorado. I mean, there can be a lot of ladybugs all at once!! Check out this picture! It tends to happen when we have really wet springs, so the ladybugs seem to manage okay as they clear the local ecosystem of aphids and then move on to other pests, and my roses certainly do great those years. We haven’t had a swarm in about a decade now because of drought, but the ladybugs in my yard certainly have been handling all of the aphids.

I guess I should go look for that ladybug again…

The BioGeek Memoirs: Pampas Grass

It’s fall now in Colorado. The evenings are crisp, the trees are glowing in autumn hues, the crickets have gone silent, and only the bunnies remain in the yard. The last of the plants in my gardens are bravely blooming still, but tomorrow there is a frost warning, and their last days are upon them.

Here and there among the glowing trees the plumes of ornamental Pampas grass wave in the wind. These showy grasses, indigenous to the Pampas region of South America, have become more and more popular over the last few years and different varieties of them wave in the wind at me as I drive by on errands. Each time I see one I’m hit with a wave of good feeling: my mother loved Pampas grass.

Remember my mom, born in Yokohama, Japan, to Swedish-American parents? Well, she spent her high school years in Buenos Aires, Argentina, at the edge of the South American Pampas. How did that happen, you ask. Well… my grandfather was an engineer who worked for a canning company that operated internationally, which is why my mom learned 4 different languages during her life. Let’s get back to the Pampas grass…

Early in the summer the grasses have these showy white plumes…
Now the plumes are brown as the seeds ripen. Do you see how tall these grasses are?
That stop sign is taller than me, so that grass is at least 8 feet tall!!

Every time my mother saw Pampas grass growing, she would exclaim about how wonderful it was, how it came from the Pampas, and then the stories about the Pampas would start. The grasslands, the Gauchos, Yerba Mate tea, ropes and cows, and then all her memories of Buenos Aires. (We tried to love the Pampas grass too, for her sake, but the edges of the grass had little buzzsaw edges that could give us a nasty cut on our fingers. Those grasses are better admired from afar!) She made us Yerba Mate tea and we could try to drink it out of her special little gourd with its silver straw.

My mom used to wear this silver brooch of a Gaucho hat with an attached rope and knife.

Now I live at the edge of the North American Great Plains which is similar to the Pampas of my mother’s formative years. Many of the animals that live here echo the animals that my mother told us about when I was young (but not all… we have bison!), and instead of Gauchos we have a Cowboy culture. There are tall grasses here, and sagebrush, but nothing like the Pampas grass. Still, there are the open skies, the gentle hills covered with waving grass, raptors soaring overhead, and the occasional sighting of an antelope or deer. I understand why my mother evidently longed for the open vistas of the Pampas after she had left them, and each time I drive past open prairielands I feel connected through time with her.

And every time I see Pampas grass.

The BioGeek Memoirs: Swallowtail and Ash

September 1st. I woke up this morning to the sound of geese flying over the house, honking away as they crossed just above the treetops. It is a bright blue day here in Colorado where I live, and the garden and the lawn are recovering after the extreme heat of the last two months. The robins are now gone, and there is just one bunny left in my yard. The fall plants are getting ready to bloom, the first golden leaves are appearing on the locust trees, and the end of summer is upon me.

The stonecrop is starting to bloom, the viburnum berries are turning red, and the last columbine blooms of the season are appearing in the cooler weather.

Monday was an exciting day for the cats as I had the ash tree out front pruned. The tree was damaged in an early heavy snowfall, and I wanted to make sure it was given every opportunity to flourish in the aftermath of losing several limbs.

I love that ash tree! I have it treated for ash borers every year (the emerald ash borer just arrived in my area of Colorado… not good news for ash trees!), and last year I even had it deep watered during the winter to protect it from drought damage. It puts shade onto my house, is an essential component of squirrel route one over the house, and serves as food for one of my favorite butterflies…

Swallowtails! Here they are feeding on my butterfly bush’s blooms.

Swallowtails are big butterflies! They are so big (they don’t hold still long enough for me to measure, but they are like 3-4 inches…) you can sometimes hear them flapping as they head across the yard, darting to and fro as they check out the various blooms in the area. They are much faster and more robust than your usual butterfly, so they are hard to grab a shot of if they don’t settle down onto a flower to snack on some nectar. They love my butterfly bushes, so I planted more last year hoping to lure them to the yard. I also left the stump of an ash tree that I lost a few years ago in the back yard, too.

This is what is left over from my lost ash tree in the back yard.

Okay, I am a geek for sure. I didn’t cut back the suckers from the stump so it would grow into a shrub with enticing ash leaves for swallowtails to lay eggs on. The shrub is also important shade for baby bunnies, but that is another issue. All that lawn damage around the shrub is from the bunnies eating the grass down to the dirt, and then rolling around in the dirt, and then doing a little digging on the side, but… this is a post about butterflies so I will move on.

Bunny: you should just move on… by the way, do you notice how cute I am?

Several times this summer I saw swallowtails in the ash shrub. Yay! The ash tree isn’t food for the butterflies, but rather food for the developing larvae from the eggs that the butterfly lays on the leaves. It is my hope that there were some eggs laid in there that will lead to new swallowtails in the spring next year. I haven’t seen any of the caterpillars, but something has been munching on the leaves…

Quite a few of the leaves show the evidence of an insect snacking on them!

The caterpillars become pupae eventually and then hide themselves away in a sheltered location for the winter, emerging as butterflies in the spring. It is my hope that there are some pupae tucked away in a bunny-proof location near the ground and along the cut-off trunk of the old tree where they will gradually transform into the fabulous flyers of the summer.

The guys who pruned the ash tree out front also removed a struggling maple tree from my back yard. They gave the ash shrub some side eye and offered to take it away too, but I was like… NOOOOOO… I need that for my backyard wildlife…

Did they not notice my butterfly bushes? This backyard is a whole butterfly ecosystem that I have going…

Summer is on the wane, and the swallowtails are gone along with the robins and almost all of my bunnies. Soon the leaves will fall. Asleep, hidden in the debris of summer, the butterflies are secretly transforming and biding their time until May. Sleep well, little guys. I can’t wait to see you next year.

The BioGeek Memoirs: Squirrel

Growing up as a little girl in Southern California I never saw many squirrels. They were this cute little animal that you might be able to see if you went up into the mountains. If you were lucky, you might be able to feed part of your lunch to a ground squirrel at a rest stop. They were rare, elusive, cute, and I absolutely, positively wanted to have one as a pet.

Look at the tail on this little guy who has been hanging out in my back yard!!

Then I moved to Colorado. Squirrels rule here!!! If you offer some food to a squirrel at a park you might get mobbed. Seriously, I had to once pick up a child and back away from the descending mob of squirrels after tossing out some scraps of bread. They are so cute, but best to not encourage them too much. They eat all the yummy food growing in gardens (ahem… strawberries and grapes… ), raid the trash, and aren’t above dragging off the dog’s Kong to get the treats inside. Bird feeders are actually squirrel feeders. These guys are so bright that it is almost impossible to keep them out of the feeders. There were some “squirrel proof” feeders at the local bird supply store, but I just laughed and bought a bird house. I love the squirrels, but I am not feeding them, because… previously mobbed by hungry squirrels…

Teenaged squirrels playing this spring on a garden chair.

Here where I live now there are squirrel nests in trees all around, and this last year a nest finally arrived in my front tree. It looks like a huge ball of leaves caught up in the branches; three cute little squirrel youngsters showed up this spring racing around the trunk, over the branches, and across the roof to my back yard where they access the fence which serves as the highway to all the other houses on my block. I call this Squirrel Route One, and the movement of little feet over the roof and the scrabble of squirrels along the fence are my morning entertainment every day while I’m outside on the deck drinking my morning latte. Why look at what has happened: I have pet squirrels after all!

The pictures show squirrels moving on Squirrel Route One: along the fence, then down into the yard to my deck, across the deck, and then a fast climb to the upper supports and a leap onto the roof. These squirrels aren’t above checking me out to see if I have some unsecured snacks. Nope, little guys. Move along!!

I do make sure that there is water for the squirrels, however.

There are several types of squirrels in Colorado, and these guys seem to be a type of tree squirrel called the fox squirrel. They provide endless entertainment for me and the cats and were great distractions (Squirrel!!!) for me as I recovered from surgery this spring. I used squirrels in my teaching; there was a white squirrel in a Denver park a few years ago, and I used the videotaped newscast about her in my biology classroom. That white squirrel wasn’t an albino as her eyes were dark, and her offspring were all normal in coloration. “What type of genetic mutation is this?” I would ask the class. (It’s recessive.) What would the Punnett square of the offspring look like? If two offspring mated (I know… icky… just go with it!) what would be the chance of another white squirrel? Is this a genetic feature that will be selected for? What if our weather changed and it was snowy all the time? The kids loved the white squirrel lesson. Well, they are so darn cute, what’s not to like?

Adult (not white) squirrel on my ash tree.

I’m not above having fun with squirrels and my neighbors. Squirrels can be enormous pests, and a few years ago they managed to work their way into my next-door neighbor’s attic where they went wild eating the wire insulation. Bad squirrels!! I printed out a recipe for squirrel pot pie and anonymously taped it to their front door. I know, I’m bad. They trapped those squirrels, repaired the roof, and I’m pretty sure that none of the squirrels became dinner. Pretty sure…

They got back by feeding the squirrels that remained lots and lots of peanuts in the shells that the squirrels buried all over my yard and in the gardens.

I gave them a little stuffed toy squirrel wearing baby booties when they had a new baby.

Squirrel wars!

That neighbor eventually moved away and just a couple of weeks ago she called me to catch up on all the neighborhood news. “I now have a squirrel nest!” I told her. They are living in a new housing area without mature trees now and there are no squirrels. They miss them.

Because squirrels are so darn cute!!

And they are favorites of watching cats everywhere!

The BioGeek Memoirs: Snapdragon

I just love snapdragons! I mean, they have those cute little faces; they do look a little like dragon faces if you use some imagination.

Snapdragon plant in my front yard.

Snapdragons are great plants for me in my gardening efforts. They are really hardy, tolerate dry conditions, and there are new varieties that are small and easy to grow in containers and along the edge of your driveway or garden. The picture above is one that is growing in the margin between my rocked-in area and the driveway; I didn’t plant this guy; it is a volunteer that sprang up from a previous year’s plantings. The original plant was something like this one… a mixture of orange, yellow and pink that changes in the flowers as they age. Pretty cool, huh. I look at the plant and wonder how/why the pigment in the flower is changing over time. BioGeek, right?! It gets even better…

All of these plants are also volunteers from the original parent plant from a couple of years ago.

Do you see all of those colors? They are the result of genetic recombination that happened in the original plant’s flowers when the plant reproduced and created the seeds that rose up to produce this array of colors. Some of the offspring have clear-colored flowers (the yellow and the red), while other have the mixed hues and color-changing characteristics of the parent plant.

Notice, I said parent plant. The funky thing about snapdragons is that they self-pollinate and reproduce on their own with the pollen getting to the stamens within the closed flower without any intervention by outside helpers like wind or insects. In fact, they are so hard to open that only a really heavy insect like a bumblebee can open the flower to get to the nectar inside. As the (big old fat) bumblebee climbs into the flower the little hairs on its body pick up pollen. When the bumblebee flies on to another snapdragon and then climbs into that flower it can carry the pollen in with it to cross-pollinate the new plant with the previous one’s pollen.

Bumblebees started showing up in my garden last week, and I would like to believe that they have been busy with the snapdragons too. If you snap open one of the flowers like I did in the picture above, you can see the pollen-carrying anthers above the opening and then waaaay down at the bottom of the flower is the nectar with the ovary. An industrious bumblebee can push open the flower and then muscle its way in to the bottom. Yay! More flower colors are on the way when there is crossbreeding among my plants. Here’s a great blog posting (Ray Cannon’s Nature Notes) showing a bumblebee taking on a snapdragon.

All this brings me to Mendel and classic genetics. Gregor Mendel (1822-1884) was a monk who had a deep interest in the science. He lived in a time when genetics was very poorly understood, and the basic question was “how are traits transmitted to new generations?” Mendel chose a plant that self-pollinated like a snapdragon (pea plants) and controlled the cross-pollination between parent plants with distinctive characteristics like the color of the flower, the height of the plant, or the color of the pea. He cut away the pollen producing structures in the flowers, used little brushes to carry pollen from one plant to another (taking on the role of the bumblebee in snapdragons), and then put little fabric hats over the flowers to prevent any other pollination from occurring. Tedious, right? Anyway, this work led to the essential understanding in basic genetics that we all now know. Some genes are dominant, and others are recessive. You have two copies of each gene (one from your mom, one from your dad), and the inheritance of which copy you got from each parent is random. Here’s an online tutorial of classic genetics maintained by the Cold Spring Harbor Laboratory.

Good thing that Mendel didn’t choose snapdragons. Snapdragons are a problem for classic genetics because their genes don’t always follow the dominant/recessive inheritance pattern. Instead, some of the colors in snapdragons are both expressed at the same time, and we call that codominant. So…. a red snapdragon crossed with a white snapdragon will produce plants with pink flowers. We now understand how and why that happens, and there are lots of other examples of non-Mendelian genetics like blood type inheritance and tortoiseshell cats. If Mendel had chosen snapdragons to study, he would have floundered around forever, but thanks to him (and pea plants) the first understandings were worked out. Think of how hard that was… no one knew what the genetic material was or had glimpsed a chromosome, but he figured out the process using his pea plant data and some truly exhausting math. Way to go, Mendel!!

Seed pods on my snapdragon plants. Those seeds carry the next generation of snapdragons waiting to grow up next year.

So, when I see my snapdragons, I am transported once again to my biology classroom and those early genetics lessons with students. I am connected to the world of science and the legacy given to me by Mendel and others. Why are my flowers a mixture of pink, yellow, and orange? Hmmm…. maybe there is more than one pigment gene at work at the same time, and the amount of pigment being produced is changed as the plant ages? Is this some funky combination of red and yellow genes? I kind of think so, since I now have plants with clear red and yellow flowers: they must have two copies of either the red or yellow gene. Is there another gene kicking in to modulate the amount of pigment produced as the flower ages? What about the pigments that I can’t see, but are there for the bees to see? This is so cool, and I just love snapdragons!!!!

This isn’t just a garden, but a genetics experiment that I’ve been running for a few years now.

Yay, science!

Thoughts on “Lessons in Chemistry” while sitting in my Garden

The monsoon has arrived in Colorado! This monsoon is not bringing any rain my way, but it is carrying in cooler air and gentle breezes through the day. Suddenly I am spending lots of time outside. I’ve worked in the gardens every single evening for a couple of hours and the gardens are actually starting to look like… gardens! Okay, I have to admit, there is still lots of work to get done, but I’m so happy to see tidy weeded gardens with lovely rose bushes without a throng of weeds around them.

In the late afternoons, when it is still a little too sunny to work in the gardens, but nice for sitting outside because my swinging garden seat is in the shade, I move out to read with the wildlife. Look at the great pictures I got this week!

My yard is a playground for a group of juvenile squirrels who are always entertaining. There are huge swallowtail butterflies and tiny birds in the yard, but those guys haven’t stopped long enough for me to get a photo yet. The robin is a regular at my little birdbath, and the first bumblebees of the year showed up to sample some of my flowers. My favorite rose bush, the Princess Alexandra of Kent, now has 15 blooms going. My back gardens are filled with new plantings, and the lavender and yarrow are just a few days away from the first blooms. I’m really enjoying my time outside reading, and then I think about the book while I pull weeds and put the gardens into order.

Lessons in Chemistry: A Novel by Bonnie Garmus has been on my mind a lot this last week. The story is of Elizabeth Zott, an intrepid individualist woman who is a scientist by nature and calling, challenged by her gender and the time in which she lived.

I just love the Elizabeth Zott character. I understand and identify with her so much. Elizabeth is a chemist/scientist trying to do research into an original area of chemistry that intersects with biology. Did I mention that it is the 50s? Oh. Elizabeth has a lot of obstacles to overcome: women are expected to be homemakers, and misogyny and gender stereotypes are everywhere. Other women gossip about her and sabotage her. Men steal her work and take credit for it. She loses her job and ends up doing a cooking show on television.

Where she teaches cooking as lessons in chemistry to produce the best, most wonderful dishes ever. Women love her show, take lecture notes through the programs, cook the meals, and learn to think differently about their abilities, their role in society, and their individual worth. The book is wonderful. The book is about keeping an open mind, questioning everything, collecting data, and thinking for oneself. Also, there is a dog who is a major character in the story and who has a wonderful voice and viewpoint of his own.

So why does this book connect so much to me? Well… I grew up in the 50s and 60s. I entered college as a chemistry major (but once I discovered molecular biology, which is kind of biological chemistry, I was gone…). We kind of forget how things used to be for women, but I do remember how things were.

A small list of events from that time:

  • The men talking out front after church each Sunday sure were critical of women drivers. Like, women shouldn’t be allowed to drive. They were serious!
  • A woman at my church had cancer. Her husband, who was in charge of her health care, had that information concealed from her.
  • My high school counselor told me that I would make a great nurse because I was so smart, I could support doctors in making their diagnoses, helping them with their careers. I decided that maybe I should be a doctor…
  • My chemistry advisor in college told me that women were just taking away a slot from a man and that the education was wasted on them because they would just become housewives. Umm… I had just made the Dean’s List…
  • I interviewed for my first research lab job after college. I had to answer a lot of questions about my husband, his career plans, and whether we would be having another child. I think that I got the job because my husband needed me to support the family while he finished college.
  • Working at my lab bench late one afternoon I overheard the head of the lab discussing the research of one of the postdoctoral fellows, a woman. They were denigrating her work while, at the same time, talking about how they could clean it up for publishing. They published her research under their own names later that year.

Well, that’s enough to give you a glimpse of what it was like for women as they struggled for equal opportunities, standards, and pay. We’ve come a long way, but the fight goes on. What I especially loved about science is that it helped level the playing field and encouraged independent, out-of-the box thinking.

Which brings me back to the book. Elizabeth reads to the dog and teaches him hundreds of words. Elizabeth allows her daughter to read just about anything that she can get her hands on (a reading philosophy that I also benefited from), and teaches her cooking show viewers to take a few minutes to savor their accomplishments. Elizabeth rows with men. Elizabeth moves through the world, astonishingly self-confident, striving always to extend the envelope of her knowledge, fearlessly challenging the status quo, viewing everything through the lens of science.

I kind of think that Elizabeth Zott is my hero!

And science. Always, science.

Cooking may be chemistry, but biology is life.

This is me, sitting in my garden, thinking about life.

The BioGeek Memoirs: American Robin

I’m sitting out in my back yard this late afternoon listening to the songs of robins. What do they sound like, you ask? Check out this link with American robins singing.

I have a lot of robins in the yard this year. I see them on the fence, running across the front yard, pulling up insects and worms from the lawn after I mow and water in the evenings, and splashing in the birdbath in my back yard.

I just love the robins! They are kind of intrepid, don’t you think? Lots of birds hop around, but no, not robins: robins are runners! I watch them run across the road almost every morning while I make my latte, and then across the lawn with a “you bunnies had better get out of my way” attitude. I mean, they are running chests out and leading with their beaks! What could be a better way to start the morning? Be like a robin, tackle each morning at a run! Be sure you get your latte first, however…

I almost never see robins over the winter, but they are kind of early arrivers in the spring. More than once, on a March snowy day, I have walked out to the car to find half a dozen male robins in the trees, heedless of any snow on the branches, carrying on and singing like crazy as they compete with the other birds. These first groups of robins are called waves, and they really are a first sign of spring.

Robins do migrate south in the winter and return to the north in the spring, but evidently it isn’t a strict north/south pattern. When I was back in the biology classroom the students and I would be on the watch for the first signs of spring in a number of categories, and the sign that I like the most was the first robin seen. The first robin of spring was a big deal for the students, and we were really on the watch starting about the first week of March each year. Students started carrying cameras with them hoping to grab a great photo.

Toy robin given to me by a student to use in the classroom. The first robin of spring!!

What? You can report the first robin seen somewhere? Yep. We made our reports to Journey North, which is an educational website where first sighting of spring in a number of categories are reported by students across the nation. Here’s the page for the American robins, and you can see the mapped data with animation here. As you might guess, the first robins are seen towards the south of the US, but then as the season progresses, they are seen further and further north. What I really love about this is that the data shows (and this is data from students all over the nation!) is that robin migration isn’t simple and clear because they tend to spread out to find food and don’t always move south. In the spring, the food becomes available as the sunlight, longer days, and earth warming moves north, and the robins follow the food.

Back to my robins in the yard this year. The fledglings left the nest this week and they have been hanging out in my yard with the bunnies and squirrels.

These little guys are hanging out hoping that one of their parents will come feed them.

I tried to snap a shot of the male feeding them, but there was so much baby-bird food-begging action and wing flapping I couldn’t get a good one before the parent flew off. Still, how cool is this? They are not all that afraid of me and seem to like hanging out with the occasional baby bunny in that side of the yard.

This summer’s baby bunny is doing great!

I have bunnies again this year! The cats are beside themselves!

I half-jokingly told a neighbor last night that I might let the backyard become a meadow. The grass is now taller than the baby bunnies and I am seeing more wildlife than usual. I’m torn, because I am making good progress weeding out my gardens this year and if I let the grass get too long, I will need some type of special mower if I change my mind down the road. What if the baby bunnies need more food? It is tempting…

Nope. As soon as I post this the mower is coming out. Run bunnies, and fledgling robins, you had better take to the wing.

The BioGeek Memoirs: Sunflower

Okay, I need to be complete upfront about this: this is a crossover post. It is going to be a total amalgamation of the Scleroderma Chronicles and The BioGeek Memoirs because I just couldn’t come up with anyway to make them separate posts. Hey, I’m a biogeek with scleroderma. It was bound to happen eventually…

So, let’s get this ball rolling by talking about bean plants. That makes a lot of sense, right? When I was a biology teacher struggling to make plants interesting and to help students understand experimental design, I came up with the genius idea of letting the students design an experiment looking at the effect of fertilizer concentration on the growth of bean plants. The students had solutions with different concentrations of Miracle Gro fertilizer available to them, and then they had to struggle with planting and growing 6 bean plants while holding all the other variables constant. The plants grew, the students measured their growth, and then they charted the growth to make decisions about the best fertilizer amount.

I had the hot idea of using an Excel spreadsheet to display the student data to the whole class. That worked great! I then combined the data from all 5 classes together and… it was a huge mess. The plants were all different heights depending on which class was collecting the data. The students weren’t making any errors; the bean plants were raising and lowering their leaves each day in circadian rhythm. Depending on the time of day, the plants were a different height. Oh. Plants can move!

Sunflowers have been on my mind a lot recently. Beautiful sunflowers, whose faces turn throughout the day to follow the sun. My cousin grew enormous sunflowers one year that towered over the other plants in the garden. Sunflowers are the symbol of Ukraine. The sweater that I am knitting right now is in the colors of a field of sunflowers with their faces in the sun.

Those aren’t sunflowers, but the colors remind me of all the “Support Ukraine” knitting that is going on right now.

There are enormous fields of sunflowers near the airport in Denver that are just spectacular in the late summer. Early one morning in late August,2014, I drove past them on my way to my first appointment with a rheumatologist; my primary care physician had referred me to a specialist after some concerning bloodwork results. I was pretty sure that this morning was going to be a turning point in my life, and I was nervous and kind of fighting off tears. Behind me the rising sun poured light onto the glowing faces of sunflowers ahead of me as far as I could see; the sight was just thrilling, and I settled right down. An hour later the rheumatologist explained that I had limited systemic sclerosis (a form of scleroderma) and Sjogren’s disease. I was prescribed medication, sent for more testing, and told to stay off the internet. I looked for the sunflowers as I drove home that afternoon, but I couldn’t see them; the fields were too far from me as I drove east. Still, just knowing they were there sort of helped. Sunflowers. They were kind of a symbol of hope and the promise that I could handle anything.

Are you ready for this? The sunflower has been chosen as a symbol for scleroderma by Scleroderma Australia. Shine like a Sunflower is their campaign this June to bring scleroderma into the light of awareness.

Just like that the sunflower became an international symbol for scleroderma. I swiped this shirt image off of Amazon.

Why a sunflower? Well, like sunflowers, we scleroderma people follow the sun. Strong sunlight is actually a problem, but the warmth… bring on the warmth! For the last few weeks, I have been recovering from surgery and waiting for my biopsy results. I have been sitting outside on my deck out of the direct sun, soaking up the heat and light. Day by day, I have been improving and no longer need daytime oxygen support. My cardiologist has restarted the medication that was halted while I was in the hospital, and it hasn’t even caused a bump in my recovery. Heat and sunlight are really making a difference.

My biopsy results arrived on the first day of June. I have developed a type of interstitial lung disease that presents as hypersensitivity pneumonia. I also have the characteristics of what the report called a vascular/collagen autoimmune disease, which is pretty much a descriptor for scleroderma. Yep. What my pulmonologist prepared me for. This is interstitial lung disease associated with system sclerosis (SSc-ILD) and I am going to get started on an increased dosage of immunosuppressants and a new drug to prevent scarring in my lungs called OFEV. This drug is really new; it has been developed in the years since my diagnosis, and now it is here just when I need it.

June is Scleroderma Awareness Month. Here in the US the theme of the campaign is Know Scleroderma. Oh, I know scleroderma, and so do some of you through my blog. Let’s put scleroderma aside for the time being and go back to sunflowers. And science. Remember that this post started with a little story about doing a science experiment with bean plants and my students? As simple as that was in my classroom, the heart of that process, curiosity, scientific experimentation, and data manipulation, is serving me well now. Ironically, new therapies and treatment approaches are being developed because of the lung scarring caused by Covid-19. Science. It rocks!

Today I planted these sunflowers along my side fence.

This afternoon I am once again outside in the warmth and light, knitting on my new sweater in the colors of sunflowers against the sky, admiring my beautiful newly planted sunflowers. They have their little faces angled to the southwest, following the sun as it starts to dip towards the Rocky Mountains.

Beautiful, tough, follow-the-sun sunflowers, reminding me to also follow the sun and to shine when I can. They remain a symbol of hope and a promise that I can handle anything.

Shine like a Sunflower.

June is Scleroderma Awareness Month. You can learn more about scleroderma at these links.